Contacts of the strand formed by residues 219 - 224 (chain D) in PDB entry 6WNX
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with LEU 219 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215D PHE* 3.0 3.9 - - - +
216D SER 2.8 40.6 + - - +
217D ASN* 4.3 3.6 - - + +
218D GLY* 1.3 78.5 - - - +
220D MET* 1.3 70.7 + - - +
221D VAL* 4.3 5.4 - - + -
231D VAL* 3.4 28.7 - - + -
232D TRP 3.0 20.0 - - - +
233D ASP* 5.4 0.9 - - - +
234D MET* 4.1 2.2 - - - +
243D ARG* 4.3 21.1 - - - +
258D PHE* 3.6 16.5 - - + -
263D ILE* 5.7 0.4 - - + -
277D THR* 3.6 31.6 - - + +
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Residues in contact with MET 220 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181D VAL* 3.6 28.5 - - + -
189D VAL* 4.4 4.0 - - + -
191D VAL* 5.6 0.9 - - + -
203D LEU* 3.3 34.1 - - + -
213D LEU* 4.7 4.5 - - + -
214D ARG 3.3 12.3 - - - +
215D PHE* 3.7 11.2 - - + -
219D LEU* 1.3 76.1 - - - +
221D VAL* 1.3 70.2 + - - +
222D THR* 4.1 16.2 - - + -
231D VAL* 3.6 0.2 - - - -
232D TRP* 2.7 51.5 + - + +
234D MET* 4.2 14.9 - - + +
240D ILE* 4.0 20.4 - - + -
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Residues in contact with VAL 221 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213D LEU* 3.1 6.8 - - - +
214D ARG 2.8 28.5 + - - +
219D LEU* 4.3 10.5 - - + -
220D MET* 1.3 79.9 - - - +
222D THR* 1.3 61.9 + - - +
229D ILE* 3.2 34.3 - - + -
230D ALA 3.2 5.8 - - - +
231D VAL* 4.5 4.7 - - + -
256D VAL* 3.5 23.5 - - + +
258D PHE* 3.6 32.1 - - + -
263D ILE* 4.3 20.0 - - + -
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Residues in contact with THR 222 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189D VAL* 3.9 23.3 - - + -
206D HIS* 2.6 31.4 + - - -
210D VAL* 4.5 3.8 - - - -
212D HIS 3.6 7.9 - - - -
213D LEU* 4.1 7.6 - - + -
220D MET* 4.1 13.7 - - + -
221D VAL* 1.3 78.6 - - - +
223D CYS* 1.3 59.3 + - - +
229D ILE* 3.2 7.8 - - - +
230D ALA* 2.8 44.3 + - - +
232D TRP* 3.2 19.5 + - + +
256D VAL* 4.6 0.7 - - - -
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Residues in contact with CYS 223 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206D HIS* 4.4 2.2 - - - -
210D VAL* 3.8 2.8 - - - +
211D LEU 3.0 22.0 + - - -
212D HIS* 3.1 37.4 + - - +
222D THR* 1.3 75.9 - - - +
224D SER* 1.3 60.8 + - - +
228D SER 3.4 7.6 - - - +
229D ILE* 4.1 6.5 - - + -
253D VAL* 3.1 42.4 - - + -
255D VAL 3.7 16.6 - - - -
256D VAL* 3.9 7.9 - - + -
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Residues in contact with SER 224 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206D HIS* 3.2 23.8 - - - -
208D GLU 2.9 12.5 + - - -
209D ALA 2.7 23.4 + - - -
210D VAL* 4.2 0.4 - - - -
211D LEU* 4.1 2.0 - - - +
223D CYS* 1.3 74.6 - - - +
225D LYS* 1.3 61.8 + - - +
226D ASP* 3.0 29.5 + - - -
227D ARG* 3.1 16.7 + - - -
228D SER 3.1 6.9 + - - -
253D VAL* 3.2 21.6 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il